1
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Zhan W, Li Z, Zhang J, Liu Y, Liu G, Li B, Shen R, Jiang Y, Shang W, Gao S, Wu H, Wang Y, Chen W, Wang Z. Energy stress promotes P-bodies formation via lysine-63-linked polyubiquitination of HAX1. EMBO J 2024; 43:2759-2788. [PMID: 38769438 PMCID: PMC11217408 DOI: 10.1038/s44318-024-00120-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
Energy stress, characterized by the reduction of intracellular ATP, has been implicated in various diseases, including cancer. Here, we show that energy stress promotes the formation of P-bodies in a ubiquitin-dependent manner. Upon ATP depletion, the E3 ubiquitin ligase TRIM23 catalyzes lysine-63 (K63)-linked polyubiquitination of HCLS1-associated protein X-1 (HAX1). HAX1 ubiquitination triggers its liquid‒liquid phase separation (LLPS) and contributes to P-bodies assembly induced by energy stress. Ubiquitinated HAX1 also interacts with the essential P-body proteins, DDX6 and LSM14A, promoting their condensation. Moreover, we find that this TRIM23/HAX1 pathway is critical for the inhibition of global protein synthesis under energy stress conditions. Furthermore, high HAX1 ubiquitination, and increased cytoplasmic localization of TRIM23 along with elevated HAX1 levels, promotes colorectal cancer (CRC)-cell proliferation and correlates with poor prognosis in CRC patients. Our data not only elucidate a ubiquitination-dependent LLPS mechanism in RNP granules induced by energy stress but also propose a promising target for CRC therapy.
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Affiliation(s)
- Wanqi Zhan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Zhiyang Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Jie Zhang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Yongfeng Liu
- Radiation Medicine Institute, The First Affiliated Hospital, ZhengZhou University, ZhengZhou, Henan, China
| | - Guanglong Liu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Bingsong Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Jinfeng Laboratory, Chongqing, China
| | - Rong Shen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Yi Jiang
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Wanjing Shang
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | - Shenjia Gao
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Han Wu
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China
| | - Ya'nan Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Wankun Chen
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Perioperative Stress and Protection, Shanghai, China.
- Department of Anesthesiology, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Zhizhang Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Jinfeng Laboratory, Chongqing, China.
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2
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Buchan JR. Stress granule and P-body clearance: Seeking coherence in acts of disappearance. Semin Cell Dev Biol 2024; 159-160:10-26. [PMID: 38278052 PMCID: PMC10939798 DOI: 10.1016/j.semcdb.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/28/2024]
Abstract
Stress granules and P-bodies are conserved cytoplasmic biomolecular condensates whose assembly and composition are well documented, but whose clearance mechanisms remain controversial or poorly described. Such understanding could provide new insight into how cells regulate biomolecular condensate formation and function, and identify therapeutic strategies in disease states where aberrant persistence of stress granules in particular is implicated. Here, I review and compare the contributions of chaperones, the cytoskeleton, post-translational modifications, RNA helicases, granulophagy and the proteasome to stress granule and P-body clearance. Additionally, I highlight the potentially vital role of RNA regulation, cellular energy, and changes in the interaction networks of stress granules and P-bodies as means of eliciting clearance. Finally, I discuss evidence for interplay of distinct clearance mechanisms, suggest future experimental directions, and suggest a simple working model of stress granule clearance.
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Affiliation(s)
- J Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85716, United States.
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3
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Kramer S, Karolak NK, Odenwald J, Gabiatti B, Castañeda Londoño P, Zavřelová A, Freire E, Almeida K, Braune S, Moreira C, Eder A, Goos C, Field M, Carrington M, Holetz F, Górna M, Zoltner M. A unique mRNA decapping complex in trypanosomes. Nucleic Acids Res 2023; 51:7520-7540. [PMID: 37309887 PMCID: PMC10415143 DOI: 10.1093/nar/gkad497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/18/2023] [Accepted: 06/06/2023] [Indexed: 06/14/2023] Open
Abstract
Removal of the mRNA 5' cap primes transcripts for degradation and is central for regulating gene expression in eukaryotes. The canonical decapping enzyme Dcp2 is stringently controlled by assembly into a dynamic multi-protein complex together with the 5'-3'exoribonuclease Xrn1. Kinetoplastida lack Dcp2 orthologues but instead rely on the ApaH-like phosphatase ALPH1 for decapping. ALPH1 is composed of a catalytic domain flanked by C- and N-terminal extensions. We show that T. brucei ALPH1 is dimeric in vitro and functions within a complex composed of the trypanosome Xrn1 ortholog XRNA and four proteins unique to Kinetoplastida, including two RNA-binding proteins and a CMGC-family protein kinase. All ALPH1-associated proteins share a unique and dynamic localization to a structure at the posterior pole of the cell, anterior to the microtubule plus ends. XRNA affinity capture in T. cruzi recapitulates this interaction network. The ALPH1 N-terminus is not required for viability in culture, but essential for posterior pole localization. The C-terminus, in contrast, is required for localization to all RNA granule types, as well as for dimerization and interactions with XRNA and the CMGC kinase, suggesting possible regulatory mechanisms. Most significantly, the trypanosome decapping complex has a unique composition, differentiating the process from opisthokonts.
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Affiliation(s)
| | - Natalia Katarzyna Karolak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | - Bernardo Gabiatti
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | | | - Anna Zavřelová
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | | | | | - Silke Braune
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Claudia Moreira
- Biocenter, University of Würzburg, Würzburg, Germany
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Amelie Eder
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Carina Goos
- Biocenter, University of Würzburg, Würzburg, Germany
| | - Mark Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Fabiola Holetz
- Carlos Chagas Institute (ICC), FIOCRUZ/PR, Curitiba, Brazil
| | - Maria Wiktoria Górna
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
| | - Martin Zoltner
- Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
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4
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Kaposi's sarcoma-associated herpesvirus (KSHV) utilizes the NDP52/CALCOCO2 selective autophagy receptor to disassemble processing bodies. PLoS Pathog 2023; 19:e1011080. [PMID: 36634147 PMCID: PMC9876383 DOI: 10.1371/journal.ppat.1011080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 01/25/2023] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) causes the inflammatory and angiogenic endothelial cell neoplasm, Kaposi's sarcoma (KS). We previously demonstrated that the KSHV Kaposin B (KapB) protein promotes inflammation via the disassembly of cytoplasmic ribonucleoprotein granules called processing bodies (PBs). PBs modify gene expression by silencing or degrading labile messenger RNAs (mRNAs), including many transcripts that encode inflammatory or angiogenic proteins associated with KS disease. Although our work implicated PB disassembly as one of the causes of inflammation during KSHV infection, the precise mechanism used by KapB to elicit PB disassembly was unclear. Here we reveal a new connection between the degradative process of autophagy and PB disassembly. We show that both latent KSHV infection and KapB expression enhanced autophagic flux via phosphorylation of the autophagy regulatory protein, Beclin. KapB was necessary for this effect, as infection with a recombinant virus that does not express the KapB protein did not induce Beclin phosphorylation or autophagic flux. Moreover, we showed that PB disassembly mediated by KSHV or KapB, depended on autophagy genes and the selective autophagy receptor NDP52/CALCOCO2 and that the PB scaffolding protein, Pat1b, co-immunoprecipitated with NDP52. These studies reveal a new role for autophagy and the selective autophagy receptor NDP52 in promoting PB turnover and the concomitant synthesis of inflammatory molecules during KSHV infection.
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5
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Qu ZL, Li YL, Gong XY, Zhao X, Sun HY, Dan C, Gui JF, Zhang YB. A finTRIM Family Protein Acquires RNA-Binding Activity and E3 Ligase Activity to Shape the IFN Response in Fish. THE JOURNAL OF IMMUNOLOGY 2022; 209:1335-1347. [DOI: 10.4049/jimmunol.2200343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/25/2022] [Indexed: 01/04/2023]
Abstract
Abstract
Tripartite motif (TRIM) family proteins have come forth as important modulators of innate signaling dependent on of E3 ligase activity. Recently, several human TRIM proteins have been identified as unorthodox RNA-binding proteins by RNA interactome analyses; however, their targets and functions remain largely unknown. FTRCA1 is a crucian carp (Carassius auratus)–specific finTRIM (fish novel TRIM) member and negatively regulates the IFN antiviral response by targeting two retinoic acid–inducible gene-I (RIG-I)–like receptor (RLR) pathway molecules, that is, TANK-binding kinase 1 (TBK1) and IFN regulatory factor 7 (IRF7). In this study, we identify FTRCA1 as an RNA-binding E3 ligase and characterize the contribution of its RNA-binding activity and E3 ligase activity to fish IFN response. Besides targeting TBK1 and IRF7, FTRCA1 downregulates fish IFN response also by targeting stimulator of IFN response cGAMP interactor 1 (STING1). E3 ligase activity is required for full inhibition on the TBK1- and IRF7-mediated IFN response, but partial inhibition on the STING1-mediated IFN response. However, FTRCA1 has a general binding potential to mRNAs in vitro, it selectively binds STING1 and IRF7 mRNAs in vivo to attenuate mRNA levels, and it directly interacts with TBK1 protein to target protein degradation for downregulating the IFN response. Our results present an interesting example of a fish species–specific finTRIM protein that has acquired RNA-binding activity and E3 ligase activity to fine-tune fish IFN response.
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Affiliation(s)
- Zi-Ling Qu
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Yi-Lin Li
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Xiu-Ying Gong
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Xiang Zhao
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Hao-Yu Sun
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Cheng Dan
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
| | - Jian-Fang Gui
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
- ‡The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Yi-Bing Zhang
- *State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- †University of Chinese Academy of Sciences, Beijing, China; and
- ‡The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
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6
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Post-Transcriptional Control of mRNA Metabolism and Protein Secretion: The Third Level of Regulation within the NF-κB System. Biomedicines 2022; 10:biomedicines10092108. [PMID: 36140209 PMCID: PMC9495616 DOI: 10.3390/biomedicines10092108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
The NF-κB system is a key transcriptional pathway that regulates innate and adaptive immunity because it triggers the activation and differentiation processes of lymphocytes and myeloid cells during immune responses. In most instances, binding to cytoplasmic inhibitory IκB proteins sequesters NF-κB into an inactive state, while a plethora of external triggers activate three complex signaling cascades that mediate the release and nuclear translocation of the NF-κB DNA-binding subunits. In addition to these cytosolic steps (level 1 of NF-κB regulation), NF-κB activity is also controlled in the nucleus by signaling events, cofactors and the chromatin environment to precisely determine chromatin recruitment and the specificity and timing of target gene transcription (level 2 of NF-κB regulation). Here, we discuss an additional layer of the NF-κB system that manifests in various steps of post-transcriptional gene expression and protein secretion. This less-studied regulatory level allows reduction of (transcriptional) noise and signal integration and endows time-shifted control of the secretion of inflammatory mediators. Detailed knowledge of these steps is important, as dysregulated post-transcriptional NF-κB signaling circuits are likely to foster chronic inflammation and contribute to the formation and maintenance of a tumor-promoting microenvironment.
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7
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Kleer M, Mulloy RP, Robinson CA, Evseev D, Bui-Marinos MP, Castle EL, Banerjee A, Mubareka S, Mossman K, Corcoran JA. Human coronaviruses disassemble processing bodies. PLoS Pathog 2022; 18:e1010724. [PMID: 35998203 PMCID: PMC9439236 DOI: 10.1371/journal.ppat.1010724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 09/02/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022] Open
Abstract
A dysregulated proinflammatory cytokine response is characteristic of severe coronavirus infections caused by SARS-CoV-2, yet our understanding of the underlying mechanism responsible for this imbalanced immune response remains incomplete. Processing bodies (PBs) are cytoplasmic membraneless ribonucleoprotein granules that control innate immune responses by mediating the constitutive decay or suppression of mRNA transcripts, including many that encode proinflammatory cytokines. PB formation promotes turnover or suppression of cytokine RNAs, whereas PB disassembly corresponds with the increased stability and/or translation of these cytokine RNAs. Many viruses cause PB disassembly, an event that can be viewed as a switch that rapidly relieves cytokine RNA repression and permits the infected cell to respond to viral infection. Prior to this submission, no information was known about how human coronaviruses (CoVs) impacted PBs. Here, we show SARS-CoV-2 and the common cold CoVs, OC43 and 229E, induced PB loss. We screened a SARS-CoV-2 gene library and identified that expression of the viral nucleocapsid (N) protein from SARS-CoV-2 was sufficient to mediate PB disassembly. RNA fluorescent in situ hybridization revealed that transcripts encoding TNF and IL-6 localized to PBs in control cells. PB loss correlated with the increased cytoplasmic localization of these transcripts in SARS-CoV-2 N protein-expressing cells. Ectopic expression of the N proteins from five other human coronaviruses (OC43, MERS, 229E, NL63 and SARS-CoV) did not cause significant PB disassembly, suggesting that this feature is unique to SARS-CoV-2 N protein. These data suggest that SARS-CoV-2-mediated PB disassembly contributes to the dysregulation of proinflammatory cytokine production observed during severe SARS-CoV-2 infection.
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Affiliation(s)
- Mariel Kleer
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Rory P. Mulloy
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Carolyn-Ann Robinson
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Danyel Evseev
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Maxwell P. Bui-Marinos
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Elizabeth L. Castle
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arinjay Banerjee
- Vaccine and Infectious Disease Organization, University of Saskatchewan; Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan; Saskatoon, Saskatchewan, Canada
- Department of Biology, University of Waterloo; Waterloo, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Karen Mossman
- Department of Medicine, Master University, Hamilton, Ontario, Canada
- Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer A. Corcoran
- Microbiology, Immunology and Infectious Diseases Department, University of Calgary, Calgary, Alberta, Canada
- Charbonneau Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada
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8
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Kedia S, Aghanoori MR, Burns KML, Subha M, Williams L, Wen P, Kopp D, Erickson SL, Harvey EM, Chen X, Hua M, Perez JU, Ishraque F, Yang G. Ubiquitination and deubiquitination of 4E-T regulate neural progenitor cell maintenance and neurogenesis by controlling P-body formation. Cell Rep 2022; 40:111070. [PMID: 35830814 DOI: 10.1016/j.celrep.2022.111070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 05/17/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022] Open
Abstract
During embryogenesis, neural stem/progenitor cells (NPCs) proliferate and differentiate to form brain tissues. Here, we show that in the developing murine cerebral cortex, the balance between the NPC maintenance and differentiation is coordinated by ubiquitin signals that control the formation of processing bodies (P-bodies), cytoplasmic membraneless organelles critical for cell state regulation. We find that the deubiquitinase Otud4 and the E3 ligase Trim56 counter-regulate the ubiquitination status of a core P-body protein 4E-T to orchestrate the assembly of P-bodies in NPCs. Aberrant induction of 4E-T ubiquitination promotes P-body assembly in NPCs and causes a delay in their cell cycle progression and differentiation. In contrast, loss of 4E-T ubiquitination abrogates P-bodies and results in premature neurogenesis. Thus, our results reveal a critical role of ubiquitin-dependent regulation of P-body formation in NPC maintenance and neurogenesis during brain development.
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Affiliation(s)
- Shreeya Kedia
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Mohamad-Reza Aghanoori
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Kaylan M L Burns
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Maneesha Subha
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Laura Williams
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Pengqiang Wen
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Drayden Kopp
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Sarah L Erickson
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Emily M Harvey
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Xin Chen
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Michelle Hua
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jose Uriel Perez
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Fatin Ishraque
- Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Guang Yang
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Owerko Centre, ACHRI, Calgary, AB T2N 4N1, Canada.
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9
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Jeon P, Ham HJ, Park S, Lee JA. Regulation of Cellular Ribonucleoprotein Granules: From Assembly to Degradation via Post-translational Modification. Cells 2022; 11:cells11132063. [PMID: 35805146 PMCID: PMC9265587 DOI: 10.3390/cells11132063] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Cells possess membraneless ribonucleoprotein (RNP) granules, including stress granules, processing bodies, Cajal bodies, or paraspeckles, that play physiological or pathological roles. RNP granules contain RNA and numerous RNA-binding proteins, transiently formed through the liquid–liquid phase separation. The assembly or disassembly of numerous RNP granules is strongly controlled to maintain their homeostasis and perform their cellular functions properly. Normal RNA granules are reversibly assembled, whereas abnormal RNP granules accumulate and associate with various neurodegenerative diseases. This review summarizes current studies on the physiological or pathological roles of post-translational modifications of various cellular RNP granules and discusses the therapeutic methods in curing diseases related to abnormal RNP granules by autophagy.
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10
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Guz M, Jeleniewicz W, Cybulski M. An Insight into miR-1290: An Oncogenic miRNA with Diagnostic Potential. Int J Mol Sci 2022; 23:ijms23031234. [PMID: 35163157 PMCID: PMC8835968 DOI: 10.3390/ijms23031234] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 12/12/2022] Open
Abstract
For more than two decades, the view of the roles of non-coding RNAs (ncRNAs) has been radically changing. These RNA molecules that are transcribed from our genome do not have the capacity to encode proteins, but are critical regulators of gene expression at different levels. Our knowledge is constantly enriched by new reports revealing the role of these new molecular players in the development of many pathological conditions, including cancer. One of the ncRNA classes includes short RNA molecules called microRNAs (miRNAs), which are involved in the post-transcriptional control of gene expression affecting various cellular processes. The aberrant expression of miRNAs with oncogenic and tumor-suppressive function is associated with cancer initiation, promotion, malignant transformation, progression and metastasis. Oncogenic miRNAs, also known as oncomirs, mediate the downregulation of tumor-suppressor genes and their expression is upregulated in cancer. Nowadays, miRNAs show promising application in diagnosis, prediction, disease monitoring and therapy response. Our review presents a current view of the oncogenic role of miR-1290 with emphasis on its properties as a cancer biomarker in clinical medicine.
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11
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A panel of KSHV mutants in the polycistronic kaposin locus for precise analysis of individual protein products. J Virol 2021; 96:e0156021. [PMID: 34936820 PMCID: PMC8906436 DOI: 10.1128/jvi.01560-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is the cause of several human cancers, including the endothelial cell (EC) malignancy, Kaposi’s sarcoma. Unique KSHV genes absent from other human herpesvirus genomes, the “K-genes,” are important for KSHV replication and pathogenesis. Among these, the kaposin transcript is highly expressed in all phases of infection, but its complex polycistronic nature has hindered functional analysis to date. At least three proteins are produced from the kaposin transcript: Kaposin A (KapA), B (KapB), and C (KapC). To determine the relative contributions of kaposin proteins during KSHV infection, we created a collection of mutant viruses unable to produce kaposin proteins individually or in combination. In previous work, we showed KapB alone recapitulated the elevated proinflammatory cytokine transcripts associated with KS via the disassembly of RNA granules called processing bodies (PBs). Using the new ΔKapB virus, we showed that KapB was necessary for this effect during latent KSHV infection. Moreover, we observed that despite the ability of all kaposin-deficient latent iSLK cell lines to produce virions, all displayed low viral episome copy number, a defect that became more pronounced after primary infection of naive ECs. For ΔKapB, provision of KapB in trans failed to complement the defect, suggesting a requirement for the kaposin locus in cis. These findings demonstrate that our panel of kaposin-deficient viruses enables precise analysis of the respective contributions of individual kaposin proteins to KSHV replication. Moreover, our mutagenesis approach serves as a guide for the functional analysis of other complex multicistronic viral loci. IMPORTANCE Kaposi’s sarcoma-associated herpesvirus (KSHV) expresses high levels of the kaposin transcript during both latent and lytic phases of replication. Due to its repetitive, GC-rich nature and polycistronic coding capacity, until now no reagents existed to permit a methodical analysis of the role of individual kaposin proteins in KSHV replication. We report the creation of a panel of recombinant viruses and matched producer cell lines that delete kaposin proteins individually or in combination. We demonstrate the utility of this panel by confirming the requirement of one kaposin translation product to a key KSHV latency phenotype. This study describes a new panel of molecular tools for the KSHV field to enable precise analysis of the roles of individual kaposin proteins during KSHV infection.
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12
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TRAF6 Phosphorylation Prevents Its Autophagic Degradation and Re-Shapes LPS-Triggered Signaling Networks. Cancers (Basel) 2021; 13:cancers13143618. [PMID: 34298830 PMCID: PMC8303406 DOI: 10.3390/cancers13143618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Here, we reveal that basal turnover and autophagy-induced decay of the ubiquitin E3 ligase TRAF6 is antagonized by IKKε-mediated phosphorylation at five serines. Phosphoproteomic experiments show that TRAF6 and its phosphorylation contribute to the remodeling of LPS- and autophagyinduced signaling networks, revealing an intricate link between inflammatory and metabolic processes that are frequently dysregulated in cancer. Abstract The ubiquitin E3 ligase TNF Receptor Associated Factor 6 (TRAF6) participates in a large number of different biological processes including innate immunity, differentiation and cell survival, raising the need to specify and shape the signaling output. Here, we identify a lipopolysaccharide (LPS)-dependent increase in TRAF6 association with the kinase IKKε (inhibitor of NF-κB kinase subunit ε) and IKKε-mediated TRAF6 phosphorylation at five residues. The reconstitution of TRAF6-deficient cells, with TRAF6 mutants representing phosphorylation-defective or phospho-mimetic TRAF6 variants, showed that the phospho-mimetic TRAF6 variant was largely protected from basal ubiquitin/proteasome-mediated degradation, and also from autophagy-mediated decay in autolysosomes induced by metabolic perturbation. In addition, phosphorylation of TRAF6 and its E3 ligase function differentially shape basal and LPS-triggered signaling networks, as revealed by phosphoproteome analysis. Changes in LPS-triggered phosphorylation networks of cells that had experienced autophagy are partially dependent on TRAF6 and its phosphorylation status, suggesting an involvement of this E3 ligase in the interplay between metabolic and inflammatory circuits.
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13
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Lavalée M, Curdy N, Laurent C, Fournié JJ, Franchini DM. Cancer cell adaptability: turning ribonucleoprotein granules into targets. Trends Cancer 2021; 7:902-915. [PMID: 34144941 DOI: 10.1016/j.trecan.2021.05.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 10/21/2022]
Abstract
Stress granules (SGs) and processing bodies (P-bodies) are membraneless cytoplasmic condensates of ribonucleoproteins (RNPs). They both regulate RNA fate under physiological and pathological conditions, and are thereby involved in the regulation and maintenance of cellular integrity. During tumorigenesis, cancer cells use these granules to thrive, to adapt to the harsh conditions of the tumor microenvironment (TME), and to protect themselves from anticancer treatments. This ability to provide multiple outcomes not only makes RNP granules promising targets for cancer therapy but also emphasizes the need for more knowledge about the biology of these granules to achieve clinical use. In this review we focus on the role of RNP granules in cancer, and on how their composition and regulation might be used to elaborate therapeutic strategies.
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Affiliation(s)
- Margot Lavalée
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Nicolas Curdy
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Camille Laurent
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France; Département de Pathologie, Centre Hospitalier Universitaire (CHU) de Toulouse, 31059 Toulouse, France
| | - Jean-Jacques Fournié
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France
| | - Don-Marc Franchini
- Cancer Research Center of Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1037, Centre National de la Recherche Scientifique (CNRS) UMR 5071, 31037 Toulouse, France; Université Toulouse III Paul Sabatier, 31330 Toulouse, France; Institut Universitaire du Cancer de Toulouse-Oncopole, 31100 Toulouse, France.
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14
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Goyani S, Roy M, Singh R. TRIM-NHL as RNA Binding Ubiquitin E3 Ligase (RBUL): Implication in development and disease pathogenesis. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166066. [PMID: 33418035 DOI: 10.1016/j.bbadis.2020.166066] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 12/14/2020] [Accepted: 12/27/2020] [Indexed: 12/20/2022]
Abstract
TRIM proteins are RING domain-containing modular ubiquitin ligases, unique due to their stimuli specific expression, localization, and turnover. The TRIM family consists of more than 76 proteins, including the TRIM-NHL sub-family which possesses RNA binding ability along with the inherent E3 Ligase activity, hence can be classified as a unique class of RNA Binding Ubiquitin Ligases (RBULs). Having these two abilities, TRIM-NHL proteins can play important role in a wide variety of cellular processes and their dysregulation can lead to complex and systemic pathological conditions. Increasing evidence suggests that TRIM-NHL proteins regulate RNA at the transcriptional and post-transcriptional level having implications in differentiation, development, and many pathological conditions. This review explores the evolving role of TRIM-NHL proteins as TRIM-RBULs, their ubiquitin ligase and RNA binding ability regulating cellular processes, and their possible role in different pathophysiological conditions.
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Affiliation(s)
- Shanikumar Goyani
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India
| | - Milton Roy
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India
| | - Rajesh Singh
- Department of Biochemistry, Faculty of Science, The M.S. University of Baroda, Vadodara 390 002, Gujarat, India.
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15
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Abstract
Enzymatic reactions and noncovalent (i.e., supramolecular) interactions are two fundamental nongenetic attributes of life. Enzymatic noncovalent synthesis (ENS) refers to a process where enzymatic reactions control intermolecular noncovalent interactions for spatial organization of higher-order molecular assemblies that exhibit emergent properties and functions. Like enzymatic covalent synthesis (ECS), in which an enzyme catalyzes the formation of covalent bonds to generate individual molecules, ENS is a unifying theme for understanding the functions, morphologies, and locations of molecular ensembles in cellular environments. This review intends to provide a summary of the works of ENS within the past decade and emphasize ENS for functions. After comparing ECS and ENS, we describe a few representative examples where nature uses ENS, as a rule of life, to create the ensembles of biomacromolecules for emergent properties/functions in a myriad of cellular processes. Then, we focus on ENS of man-made (synthetic) molecules in cell-free conditions, classified by the types of enzymes. After that, we introduce the exploration of ENS of man-made molecules in the context of cells by discussing intercellular, peri/intracellular, and subcellular ENS for cell morphogenesis, molecular imaging, cancer therapy, and other applications. Finally, we provide a perspective on the promises of ENS for developing molecular assemblies/processes for functions. This review aims to be an updated introduction for researchers who are interested in exploring noncovalent synthesis for developing molecular science and technologies to address societal needs.
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Affiliation(s)
- Hongjian He
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Meihui Yi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Adrianna N Shy
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
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16
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Zarnack K, Balasubramanian S, Gantier MP, Kunetsky V, Kracht M, Schmitz ML, Sträßer K. Dynamic mRNP Remodeling in Response to Internal and External Stimuli. Biomolecules 2020; 10:biom10091310. [PMID: 32932892 PMCID: PMC7565591 DOI: 10.3390/biom10091310] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023] Open
Abstract
Signal transduction and the regulation of gene expression are fundamental processes in every cell. RNA-binding proteins (RBPs) play a key role in the post-transcriptional modulation of gene expression in response to both internal and external stimuli. However, how signaling pathways regulate the assembly of RBPs with mRNAs remains largely unknown. Here, we summarize observations showing that the formation and composition of messenger ribonucleoprotein particles (mRNPs) is dynamically remodeled in space and time by specific signaling cascades and the resulting post-translational modifications. The integration of signaling events with gene expression is key to the rapid adaptation of cells to environmental changes and stress. Only a combined approach analyzing the signal transduction pathways and the changes in post-transcriptional gene expression they cause will unravel the mechanisms coordinating these important cellular processes.
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Affiliation(s)
- Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt a.M., Germany;
| | | | - Michael P. Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia;
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3800, Australia
| | - Vladislav Kunetsky
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
| | - Michael Kracht
- Rudolf Buchheim Institute of Pharmacology, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - M. Lienhard Schmitz
- Institute of Biochemistry, FB11, Justus Liebig University, 35392 Giessen, Germany;
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany;
- Correspondence:
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17
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Semmler S, Gagné M, Garg P, Pickles SR, Baudouin C, Hamon-Keromen E, Destroismaisons L, Khalfallah Y, Chaineau M, Caron E, Bayne AN, Trempe JF, Cashman NR, Star AT, Haqqani AS, Durcan TM, Meiering EM, Robertson J, Grandvaux N, Plotkin SS, McBride HM, Vande Velde C. TNF receptor-associated factor 6 interacts with ALS-linked misfolded superoxide dismutase 1 and promotes aggregation. J Biol Chem 2020; 295:3808-3825. [PMID: 32029478 DOI: 10.1074/jbc.ra119.011215] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/17/2020] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease, characterized by the selective loss of motor neurons leading to paralysis. Mutations in the gene encoding superoxide dismutase 1 (SOD1) are the second most common cause of familial ALS, and considerable evidence suggests that these mutations result in an increase in toxicity due to protein misfolding. We previously demonstrated in the SOD1G93A rat model that misfolded SOD1 exists as distinct conformers and forms deposits on mitochondrial subpopulations. Here, using SOD1G93A rats and conformation-restricted antibodies specific for misfolded SOD1 (B8H10 and AMF7-63), we identified the interactomes of the mitochondrial pools of misfolded SOD1. This strategy identified binding proteins that uniquely interacted with either AMF7-63 or B8H10-reactive SOD1 conformers as well as a high proportion of interactors common to both conformers. Of this latter set, we identified the E3 ubiquitin ligase TNF receptor-associated factor 6 (TRAF6) as a SOD1 interactor, and we determined that exposure of the SOD1 functional loops facilitates this interaction. Of note, this conformational change was not universally fulfilled by all SOD1 variants and differentiated TRAF6 interacting from TRAF6 noninteracting SOD1 variants. Functionally, TRAF6 stimulated polyubiquitination and aggregation of the interacting SOD1 variants. TRAF6 E3 ubiquitin ligase activity was required for the former but was dispensable for the latter, indicating that TRAF6-mediated polyubiquitination and aggregation of the SOD1 variants are independent events. We propose that the interaction between misfolded SOD1 and TRAF6 may be relevant to the etiology of ALS.
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Affiliation(s)
- Sabrina Semmler
- Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec H3A 2B4, Canada.,Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada
| | - Myriam Gagné
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Pranav Garg
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Sarah R Pickles
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Charlotte Baudouin
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada.,Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Emeline Hamon-Keromen
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada.,Université Pierre et Marie Curie, 75005 Paris, France
| | - Laurie Destroismaisons
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada
| | - Yousra Khalfallah
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada.,Department of Neurosciences, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Mathilde Chaineau
- Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec H3A 2B4, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Elise Caron
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada
| | - Andrew N Bayne
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Neil R Cashman
- Department of Medicine (Neurology), University of British Columbia and Vancouver Coastal Health Research Institute, Brain Research Centre, Vancouver, British Columbia V6T 2B5, Canada
| | - Alexandra T Star
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - Arsalan S Haqqani
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - Thomas M Durcan
- Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec H3A 2B4, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Elizabeth M Meiering
- Department of Chemistry, Guelph-Waterloo Centre for Graduate Work in Chemistry and Biochemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario M5T 0S8, Canada
| | - Nathalie Grandvaux
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Heidi M McBride
- Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec H3A 2B4, Canada.,Montreal Neurological Institute, McGill University, Montréal, Quebec H3A 2B4, Canada
| | - Christine Vande Velde
- Centre de Recherche du Centre Hospitalier de Université de Montréal, Montréal, Quebec H2X 0A9, Canada .,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada.,Department of Neurosciences, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
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18
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Single-Cell Analysis of Multiple Steps of Dynamic NF-κB Regulation in Interleukin-1α-Triggered Tumor Cells Using Proximity Ligation Assays. Cancers (Basel) 2019; 11:cancers11081199. [PMID: 31426445 PMCID: PMC6721548 DOI: 10.3390/cancers11081199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/02/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
The frequently occurring heterogeneity of cancer cells and their functional interaction with immune cells in the tumor microenvironment raises the need to study signaling pathways at the single cell level with high precision, sensitivity, and spatial resolution. As aberrant NF-κB activity has been implicated in almost all steps of cancer development, we analyzed the dynamic regulation and activation status of the canonical NF-κB pathway in control and IL-1α-stimulated individual cells using proximity ligation assays (PLAs). These systematic experiments allowed the visualization of the dynamic dissociation and re-formation of endogenous p65/IκBα complexes and the nuclear translocation of NF-κB p50/p65 dimers. PLA combined with immunostaining for p65 or with NFKBIA single molecule mRNA-FISH facilitated the analysis of (i) further levels of the NF-κB pathway, (i) its functionality for downstream gene expression, and (iii) the heterogeneity of the NF-κB response in individual cells. PLA also revealed the interaction between NF-κB p65 and the P-body component DCP1a, a new p65 interactor that contributes to efficient p65 NF-κB nuclear translocation. In summary, these data show that PLA technology faithfully mirrored all aspects of dynamic NF-κB regulation, thus allowing molecular diagnostics of this key pathway at the single cell level which will be required for future precision medicine.
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19
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Mikuda N, Kolesnichenko M, Beaudette P, Popp O, Uyar B, Sun W, Tufan AB, Perder B, Akalin A, Chen W, Mertins P, Dittmar G, Hinz M, Scheidereit C. The IκB kinase complex is a regulator of mRNA stability. EMBO J 2018; 37:embj.201798658. [PMID: 30467221 DOI: 10.15252/embj.201798658] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 10/01/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022] Open
Abstract
The IκB kinase (IKK) is considered to control gene expression primarily through activation of the transcription factor NF-κB. However, we show here that IKK additionally regulates gene expression on post-transcriptional level. IKK interacted with several mRNA-binding proteins, including a Processing (P) body scaffold protein, termed enhancer of decapping 4 (EDC4). IKK bound to and phosphorylated EDC4 in a stimulus-sensitive manner, leading to co-recruitment of P body components, mRNA decapping proteins 1a and 2 (DCP1a and DCP2) and to an increase in P body numbers. Using RNA sequencing, we identified scores of transcripts whose stability was regulated via the IKK-EDC4 axis. Strikingly, in the absence of stimulus, IKK-EDC4 promoted destabilization of pro-inflammatory cytokines and regulators of apoptosis. Our findings expand the reach of IKK beyond its canonical role as a regulator of transcription.
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Affiliation(s)
- Nadine Mikuda
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marina Kolesnichenko
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Patrick Beaudette
- Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Oliver Popp
- Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Bora Uyar
- Bioinformatics/Mathematical Modelling Platform, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Wei Sun
- Laboratory for Functional Genomics and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ahmet Bugra Tufan
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Björn Perder
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Altuna Akalin
- Bioinformatics/Mathematical Modelling Platform, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Wei Chen
- Laboratory for Functional Genomics and Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Philipp Mertins
- Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Gunnar Dittmar
- Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Michael Hinz
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Claus Scheidereit
- Signal Transduction Laboratory, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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20
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Qi MY, Song JW, Zhang Z, Huang S, Jing Q. P38 activation induces the dissociation of tristetraprolin from Argonaute 2 to increase ARE-mRNA stabilization. Mol Biol Cell 2018; 29:988-1002. [PMID: 29444957 PMCID: PMC5896936 DOI: 10.1091/mbc.e17-02-0105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
ARE-mRNAs are actively degraded with tristetraprolin (TTP) in resting cells while they turn into stable messengers in activated cells. P38 plays a crucial role in stabilizing ARE-mRNA. Here we reveal that P38 activation represses the interaction between TTP and Ago2, thus restraining TTP from being targeted into processing bodies and stabilizing ARE-mRNA.
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Affiliation(s)
- Mei-Yan Qi
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing-Wen Song
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China
| | - Zhuo Zhang
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China.,Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai 200237, China
| | - Shuang Huang
- Department of Cardiology, Changhai Hospital, Shanghai 200433, China
| | - Qing Jing
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Cardiology, Changhai Hospital, Shanghai 200433, China
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21
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Romero-Barrios N, Vert G. Proteasome-independent functions of lysine-63 polyubiquitination in plants. THE NEW PHYTOLOGIST 2018; 217:995-1011. [PMID: 29194634 DOI: 10.1111/nph.14915] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/12/2017] [Indexed: 05/21/2023]
Abstract
Contents Summary 995 I. Introduction 995 II. The plant Ub machinery 996 III. From Ub to Ub linkage types in plants 997 IV. Increasing analytical resolution for K63 polyUb in plants 998 V. How to build K63 polyUb chains? 998 VI. Cellular roles of K63 polyUb in plants 999 VII. Physiological roles of K63 polyUb in plants 1004 VIII. Future perspectives: towards the next level of the Ub code 1006 Acknowledgements 1006 References 1007 SUMMARY: Ubiquitination is a post-translational modification essential for the regulation of eukaryotic proteins, having an impact on protein fate, function, localization or activity. What originally appeared to be a simple system to regulate protein turnover by the 26S proteasome is now known to be the most intricate regulatory process cells have evolved. Ubiquitin can be arranged in countless chain assemblies, triggering various cellular outcomes. Polyubiquitin chains using lysine-63 from ubiquitin represent the second most abundant type of ubiquitin modification. Recent studies have exposed their common function in proteasome-independent functions in non-plant model organisms. The existence of lysine-63 polyubiquitination in plants is, however, only just emerging. In this review, we discuss the recent advances on the characterization of ubiquitin chains and the molecular mechanisms driving the formation of lysine-63-linked ubiquitin modifications. We provide an overview of the roles associated with lysine-63 polyubiquitination in plant cells in the light of what is known in non-plant models. Finally, we review the crucial roles of lysine-63 polyubiquitin-dependent processes in plant growth, development and responses to environmental conditions.
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Affiliation(s)
- Natali Romero-Barrios
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Grégory Vert
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
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22
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RNA-binding proteins control gene expression and cell fate in the immune system. Nat Immunol 2018; 19:120-129. [PMID: 29348497 DOI: 10.1038/s41590-017-0028-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 12/19/2022]
Abstract
RNA-binding proteins (RBPs) are essential for the development and function of the immune system. They interact dynamically with RNA to control its biogenesis and turnover by transcription-dependent and transcription-independent mechanisms. In this Review, we discuss the molecular mechanisms by which RBPs allow gene expression changes to occur at different speeds and to varying degrees, and which RBPs regulate the diversity of the transcriptome and proteome. These proteins are nodes for integration of transcriptional and signaling networks and are intimately linked to intermediary metabolism. They are essential components of regulatory feedback mechanisms that maintain immune tolerance and limit inflammation. The role of RBPs in malignancy and autoimmunity has led to their emergence as targets for the development of new therapeutic modalities.
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24
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Abstract
Processing bodies (P-bodies) are cytoplasmic ribonucleoprotein (RNP) granules primarily composed of translationally repressed mRNAs and proteins related to mRNA decay, suggesting roles in post-transcriptional regulation. P-bodies are conserved in eukaryotic cells and exhibit properties of liquid droplets. However, the function of P-bodies in translational repression and/or mRNA decay remains contentious. Here we review recent advances in our understanding of the molecular composition of P-bodies, the interactions and processes that regulate P-body liquid-liquid phase separation (LLPS), and the cellular localization of mRNA decay machinery, in the context of how these discoveries refine models of P-body function.
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Affiliation(s)
- Yang Luo
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Zhenkun Na
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Sarah A Slavoff
- Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States.,Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06529 , United States
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25
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Lalani AI, Zhu S, Gokhale S, Jin J, Xie P. TRAF molecules in inflammation and inflammatory diseases. ACTA ACUST UNITED AC 2017. [PMID: 29527458 DOI: 10.1007/s40495-017-0117-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Purpose of Review This review presents an overview of the current knowledge of TRAF molecules in inflammation with an emphasis on available human evidence and direct in vivo evidence of mouse models that demonstrate the contribution of TRAF molecules in the pathogenesis of inflammatory diseases. Recent Findings The tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of cytoplasmic proteins was initially identified as signaling adaptors that bind directly to the intracellular domains of receptors of the TNF-R superfamily. It is now appreciated that TRAF molecules are widely employed in signaling by a variety of adaptive and innate immune receptors as well as cytokine receptors. TRAF-dependent signaling pathways typically lead to the activation of nuclear factor-κBs (NF-κBs), mitogen-activated protein kinases (MAPKs), or interferon-regulatory factors (IRFs). Most of these signaling pathways have been linked to inflammation, and therefore TRAF molecules were expected to regulate inflammation and inflammatory responses since their discovery in 1990s. However, direct in vivo evidence of TRAFs in inflammation and especially in inflammatory diseases had been lacking for many years, partly due to the difficulty imposed by early lethality of TRAF2-/-, TRAF3-/-, and TRAF6-/- mice. With the creation of conditional knockout and lineage-specific transgenic mice of different TRAF molecules, our understanding about TRAFs in inflammation and inflammatory responses has rapidly advanced during the past decade. Summary Increasing evidence indicates that TRAF molecules are versatile and indispensable regulators of inflammation and inflammatory responses and that aberrant expression or function of TRAFs contributes to the pathogenesis of inflammatory diseases.
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Affiliation(s)
- Almin I Lalani
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Sining Zhu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Samantha Gokhale
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, New Jersey 08854
| | - Juan Jin
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Department of Pharmacology, Anhui Medical University, Meishan Road 81st, Shushan District, Hefei, Anhui province, China
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854
- Member, Rutgers Cancer Institute of New Jersey
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Valkov E, Jonas S, Weichenrieder O. Mille viae in eukaryotic mRNA decapping. Curr Opin Struct Biol 2017; 47:40-51. [PMID: 28591671 DOI: 10.1016/j.sbi.2017.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022]
Abstract
Cellular mRNA levels are regulated via rates of transcription and decay. Since the removal of the mRNA 5'-cap by the decapping enzyme DCP2 is generally an irreversible step towards decay, it requires regulation. Control of DCP2 activity is likely effected by two interdependent means: by conformational control of the DCP2-DCP1 complex, and by assembly control of the decapping network, an array of mutually interacting effector proteins. Here, we compare three recent and conformationally distinct crystal structures of the DCP2-DCP1 decapping complex in the presence of substrate analogs and decapping enhancers and we discuss alternative substrate recognition modes for the catalytic domain of DCP2. Together with structure-based insight into decapping network assembly, we propose that DCP2-mediated decapping follows more than one path.
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Affiliation(s)
- Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Stefanie Jonas
- Institute of Biochemistry, ETH Zürich, Otto-Stern Weg 3, 8093 Zürich, Switzerland.
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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